The Thosand Ninja
by Painsake
Summary: What if Naruto wasn't alone, what if he had Iruka from the start? When the kyuubi attacked, a Genin had the task of aiding a pregnant woman for the day. That task left him with secrets, blood, and the fate of the greatest shinobi's legacy on his hands.


The Thousand Ninja

What if Naruto wasn't alone? If he had a parental influence as a child? If Naruto had been adopted by Iruka?

**1.) From one to more than one**

_For the Sake of Pain_

* * *

Iruka looked at the child he had been given almost four years ago. It was their first day at the academy. He was going to be an instructor and Naruto a student.

Naruto bounced as he walked. He was in a black Jumpsuit, red vest, and orange leg warmers. Why the boy had been so insistent about the orange was an oddity to Iruka. But at least he didn't color his whole jumpsuit.

He was so cheerful and happy to finally be going to the academy. It was as if he was just a normal child.

For a moment Iruka saw himself five years ago. When the decision had been made final.

0o0o0

It had been a year since the Kyuubi had attacked and he had made genin. He had asked the Sandaime, but he wouldn't be allowed to care for the baby until the Hokage thought he was ready. The Hokage and several others in the office had appointed him to be the guardian of the host Naruto.

Due to him already knowing about _that_ and having been there when it happened. They believed that Iruka, the only one to have ever visited the boy and cared for him, having bought him several toys, would be able to give him the proper upbringing he needed.

They would prepare him with Chunin level training by the Famous copycat ninja in order to get him ready to protect the boy and have him at Chunin level. And in one year the child would go home with him.

0o0o0

The morning had passed by quickly, and for the most part uneventfully, but after the lunch break they headed outside for taijutsu.

It was the first day so they wouldn't actually train but they would be evaluated, laps, jumps, things like that.

However when Naruto came out for this Iruka could already see trouble, so he followed them out to watch. And the taijutsu instructor Mizuki, informed him that he refused to train _him._ Iruka argued with him about it, wasn't Mizuki his friend, didn't he trust the fourth? He tried but it was all in vain and finally he gave up.

0o0o0

There was another special case. One that looked as if he'd be stuck to only taijutsu already, and he had heard that the sublime green beast, Maito Gai had his eye on that one. That was it! Iruka decided to ask him. If the Sublime Green beast would train both of them.

0o0o0

It had been relatively easy to find him, but once he did he had second thoughts. At least now he knew why the man was called a green beast.

It took almost half an hour before the jonin let him get to the point of discussion, and once he did, Gai was exceptionally enthusiastic about the situation. And they agreed that when he did not have a mission he would train them in taijutsu before the academy started. And Iruka would commission it as an academy expense.

Once the deal was struck Iruka excused himself to start the paperwork. He still wasn't sure if Gai had been making fun of him for having a son when he'd never even once gotten a date. Or if that had been a subtle hint that he needed a life.

0o0o0

After the first morning of Naruto's new taijutsu training, Iruka carried Naruto home to get ready for the academy. The poor little genin to be was exhausted, and it wasn't even eight in the morning.

Iruka's worries about how Naruto's study habits would be affected were interrupted when his little charge made a declaration.

"You know what? I'm going to be Hokage!"

"Yes, I know, you've told me that several times"

"Right! But this time, when I become Hokage, I'm gonna make the giant green jerk go on missions that make _him_ run, the whole way too, and he won't even get a break when he gets there cause I'll put a time limit on him."

Iruka could only chuckle at that, but it did seem he would be great in taijutsu.

0o0o0

The years at the academy went by and Naruto got stronger. But, instead of going for top of the class, he took a low C. Iruka knew he could do it. And since his taijutsu was coming from else ware, he never got evaluated in that area. So he passed as an average student for most of the years.

His ninjutsu was a problem though. They worked to control his massive chakra months after it was introduced, but finally he was able to do the henge, although, its result was rather embarrassing. The first time he shouted sex change jutsu in class Iruka had passed out.

When he came to he gave Naruto the worst ass kicking he'd ever get from his dad.

He did this by having his perverted little son, show his new skill to their local anbu, Neko-chan. Once that was cleared up, Iruka said good by to Neko and gave Naruto "the talk."

0o0o0

The next day they were summoned to the Hokage's office, and both of them were sporting blushes.

As they entered, He introduced his son to the Third Hokage, and he remembered how he had told the Hokage he wanted Naruto.

0o0o0

He had carried _that_ book with him ever since _that_ day, and he visited baby Naruto as often as he could. But he began to notice the general discontent among his care taker. And that the only things the baby had were those that he brought. It seemed that every body else just hated the little guy.

He couldn't stay there very much longer. So Iruka requested to see the Hokage, and was taken to him instantly. Almost as if he had been expected. He told him how Naruto was being treated like he had a disease and how it seemed the care takers had just been there on order.

Then he got out the book and told him that he wanted to be the one who would teach Naruto to be the ninja Kushina had always wanted him to be. He had to be the best, like his dad was, and stubborn like his mom. If that was ever going to happen, he had to have a better child hood then he was being provided.

The Sandaime listened and nodded in agreement, once he had finished the old man spoke, as if he had practiced this speech in front of a mirror.

"hehem, Well Iruka-kun, I am greatly relieved that someone care so much about little Naruto-chan. However so far you are the only one to bring this concern to me, and I have very limited option's as to who I can trust with the child."

There it was the line that changed his path in life. "I'll do it! He needs some—"

He was going to continue and argue the reason that he should be given the chance but lost all of his words when the Hokage's aged face lit up in a smile that hadn't been seen since the last war.

0o0o0

In the office with the Hokage was also someone both Iruka and his son were a little scared of, and more than embarrassed to see. Anbu officer Neko dubbed by the blonde, 'The angry cat lady'. She was silent and gorgeous, to Iruka, but Little Naruto didn't see it. He was too busy hiding from her in his floor colored blanket. It looked as if the floor had a lump in it. And the lump was shaking in fear.

"Naruto-kun if you don't mind we must discuss the unique jutsu you created the other day."

"I'm sorry I won't do it again! Just don't let the angry cat lady get me!"

"Naruto I don't think you're in trouble or she would have already gotten you." Iruka pulled the blanket off of the boy and yanked him to a standing position.

"Well Naruto-kun, it was brought to my attention that as an act of discipline, one of my anbu assaulted you, with the permission of your father of course. And during the assault you were able to maintain a gender altering henge."

He waited for a confirming nod, before continuing.

"Now Naruto-kun, as … ill-mannered as your jutsu was, Neko-chan here, did find something interesting about it."

"Hentai."

With that word Naruto had made all three adults slam their heads into the nearest hard surface. For the Hokage it was his desk, for Neko it was the wall, Iruka however planted his face in the floor.

"No Naruto, not _that. _She found out that your henge doesn't have the same qualities as a henge." The blushing Hokage replied.

"If you don't mind showing use the henge again?" He requested. And immediately Neko added, "With cloths on this time!"

After a moment of examining the henge, the Hokage order his secretary to "Send her in."

'Her' turned out to be a teenage girl, a Chunin, and probably a new one. Her dark hair was in a long tail behind her head and her cheeks bore the Inuzuka clan tattoo.

"This is Hana Inuzuka; she will be replacing your physician. Her clan has requested that she take a position as a clan veterinarian"

Both Naruto and Iruka shot him a glare.

"However she displayed an interest and talent for medical field jutsu. Therefore I have decided to assign her as your new doctor, you will be her only patient and she will take good care of any more… mishaps you have."

"This will begin with a physical, in your current state and in your normal one as well. I have also requested that she explain certain issues to you about your actions."

Hearing that Naruto flinched, he hoped she wouldn't be 'explaining' the same way the angry cat lady did.

0o0o0

As it turned out, the henge was just what the Hokage had thought… an actual sex change jutsu. Physically altering Naruto's body however he wanted, and undetectable by medical diagnostic. Simply put he had really turn into a girl.

And the explanation hadn't been a punishment. Instead it was a repeat of his dad's lecture last night. As well as some information about the female form that hadn't been included.

Hana had assumed that this was to be used as an infiltration jutsu and began teaching him as such. She had told him so much about girls that he was beginning to wish he had never made the jutsu all over again.

With this knowledge, Naruto's life did become easier though. He decided to use it to go around town as a little girl. With deep red hair and a small form, she looked to be about two years younger than Naruto and she was nowhere near developed as Naruto's first form.

So far only seven people knew of it. The five of them were the firsts, but two others had caught him.

One was a tall one eyed jonin with a mask. He saw it and told the kid he was a genus.

The second was one of Naruto's classmates, a little girl named by her pink hair; they had attended the same kunoichi only lesson together. And when she saw it, Naruto thought she'd tell everybody. But she never did.

0o0o0

The years went by and the day finally came when Naruto would graduate. Again. He had failed twice now. Because he couldn't get the stupid bunshin. The rest of his classmates were arriving now and he sat there waiting. He had been getting ready for this the whole last year. There was no way he'd fail it this time.

"Move it pervert!" Came a scream from the door, next thing he knew, he hit the floor.

"Sakura-chan, your so mean… "Looking up at her he knew she didn't mean it, she had kept his secret for the last few years and never once did she treat him bad, as long as he didn't get in between her… and duckbutt.

That was the only kid he ever beat in a spar. His normal routine was to push them to their absolute limits before letting them win, but this Teme was just too arrogant for his own good.

So Naruto took it upon himself to correct that and lower the kid's ego. Not that it was hard; he hadn't had a good fight since Lee became the beautiful blue beast.

After he had graduated Naruto was placed back into the academy taijutsu classes. He held the record for longest matches and for least wins, of course there was the fact that he never won outside of his matches with Uchiha Sasuke. It hurt his grade but he didn't care.

0o0o0

Iruka stepped into the classroom to a great disorder. His son was on the floor and all but three of the girls were surrounding the young Uchiha. The Inuzuka heir was currently harassing one of the three sane girls. The Nara heir had actually brought a pillow and lay down on the desk to nap. _**Kami!**_ That kid could sleep through anything! And above it all was a single thing that made him angrier than the rest. Mizuki was nowhere to be seen. He had been told not to leave them unattended but he did anyway.

"**Every body shut you mouths and get in a seat!"**

That was all it took to clear the rest of the class's disorder, one simple voice amplification and a giant head genjutsu. What was Mizuki so afraid of?

Once he did arrive they began the tests and went through them pretty quickly. All of the students were able to pass the final genin exam. It seemed too easy.

Iruka could only hope that this year Naruto found it as easy as the rest of them.

And speak of the Shinigami, it was his turn.

Naruto was now older and taller. He was second tallest in the class just under the Nara heir.

He wore a black suit, which consisted of high density fabric pants and a long sleeve, high collared, shirt made of many layered extremely dense chain mesh.

And a bright velvet red open vest that only went from his shoulders to his abdomen. On the back of the vest was the Uzumaki family crest, in honor of his mother's home village. It was a red swirl only visible due to the black outline.

Too finish this look he wore a pair of orange leg warmers and forearm braces that hid his weights, and a sky blue belt. That, with his bright golden hair made it the most bizarre ninja outfit ever employed in the leaf village. Worse than even the green and blue taijutsu beasts, in their respective spandex jumpsuits.

"Alright Naruto, you know what you have to do. Just concentrate and make three bunshin, and you'll be finished. You'll be a Ninja of the leaf. You can do this."

With a nod the genin to be formed the symbols and began to mold chakra. They waited as he did this, willing to give him as much time as he needed. If he could pull this he would be rookie of the year.

The time had come for him to be a ninja! And so with a shout and a large puff of smoke he created the three bunshin required for this test! And they … were less then acceptable. Two were on the ground sick. One was able to stand but he was pale and deformed.

"I'm sorry Naruto, I though you could get it this time."

"Oh cut him some slack! Iruka, he's your son!"

"All the more reason to only accept the best from him. I am sorry, but if you can make those three then you won't be able to advance."

Watching Naruto flee the classroom cut into him like a knife, but he had to protect him.

0o0o0

_That_ day, had been so much like this one. Iruka thought back, to when he had first met Naruto.

There was some big event for the village and to celebrate it the fourth Hokage had allowed all the graduating year academy student to perform actual missions. He hadn't found out until later that the event had been the birth of the Yondaime's son. And that they were really only doing missions so that all the real ninja could be put on duty.

They had all been taken to the mission hall. The Hokage himself was there! There they were given their first D-rank missions. Most of which turned out to be simple chores around the village. But they got to get out of class and they learned how to go through the mission protocol.

This was going to be an awesome day… then Iruka saw his mission. Catching a cat! He was the rookie of the year and they wanted him to catch a cat!

He decided to ask for something else he was polite about it but the basic message was still, "I want a real ninja mission!"

The Jonin who he would later meet as Kakashi, turned to the Yondaime, "Sensei this one wants a real Ninja mission. I don't think he's met Tora yet."

At the time Kakashi had been expecting the Hokage to explain the demon powers that resided in the wife of the daimyo's cat.

Instead he got the mission that began it all. "Ok, your skills look clean enough, how about guard duty?" The Hokage had given him a smile and tilted his head waiting for an answer, but all he could do was nod.

"Good, there's a young woman in the village who has requested a bodyguard, I'll escort you there myself." He placed his hand on Iruka's shoulder and in the next instant they were in front of a house and a woman was just locking the door. In the end his mission turned out to be helping out some pregnant lady!

The day went on and he did everything she asked, finally she felt a contraction. And so they followed a elderly woman through the village.

As they passed through the Uchiha district though the elder told her to rest on a bench. One of the women there made her way over, she held a new born baby, and so they sat and talked. Having little to do he looked to the elder woman for a task and the elder told him to just relax and enjoy the peace.

This must have gotten the pregnant ladies attention because she exclaimed "ohw, you poor boy. I forgot, it must be horrible listening to us old Ladies gabbing." She handed him a book out of her Purse

"Here, this book is a very special one. In fact," she looked down and rubbed her swollen belly "I'm naming my son after the hero. You go ahead and read."

The book was titled "Tales of the Utterly Gutsy Ninja"

0o0o0

"Hey Naruto," The depressed gaki didn't even look up. "What do you want sensei"

"Naruto your dad isn't trying to be mean, or to hold you back… Its just that he lost everybody that day, his parents, his friends, your mom… he is just trying to protect you, you know that right?"

"Yeah, but I was so sure! I got every thing down perfect. And I still couldn't do it, I just can't perform that jutsu Mizuki-Sensei"

Sitting down next to him, Mizuki put his arm around the boy, "Look you just need to prove that you can handle your self with out it. And I've already talked to the Hokage about it. We decided to give you a practical exam that will prove to your dad that you done need that jutsu. Besides, you did everything else at a perfect score."

0o0o0

Iruka followed the trail, until he came upon his son. This time he had gone too far. How could he do this?

There he was, the pissed Chunin dropped to the ground behind his son.

"Naruto! What the hell do you think your doing steeling the forbidden scoll? Don't you know how big a shit-heap your going to be in!"

"Haha, hey dad I passed! I was able to finish the practical exam."

That made the storming Father draw up short. "What exam?"

"You know the one Mizuki-Sensei and Hokage-Jiji gave me"

Oh… this was bad… this was very, _very_ bad.

"Eh… dad, Is something wrong? I though you'd be proud of me."

"Naruto get down!" They both hit the ground and the blade headed for Naruto missed by several feet.

"Mizuki, I'm disappointed in you. I thought you realized how stupid you were being." Iruka stood and looked at the advancing Chunin.

After the first few years of the academy Mizuki stopped hating Naruto and admitted to him that he had just been scared that the beast would get out. They became friends and ever worked together on some of the pranks Naruto would pull. But this was no prank.

"Naruto, Mizuki lied there is no exam; he was just tricking you into committing a capital offence. I want you to take the scroll and find the Hokage, if another shinobi stops you surrender and request to be taken to the Hokage. But don't hand the scroll over to anybody."

Naruto wasn't sure what was going on but that his uncle Mizuki could use him like this was impossible to him. "O-okay" Never the less his dad would never lie to him.

As Naruto jumped up into the trees he heard Mizuki shout wait Naruto, "Iruka doesn't know. He wasn't told about the exam!"

That made sense, but since when did Mizuki refer to his dad as Iruka, when talking to him?

"Naruto I told you to go, he's telling you nothing but lies." Naruto knew that it would be handled and turned once more to leave but before landed on his next branch it exploded into pieces.

Seeing the boy leave Mizuki had realized he'd lost the game and from here on he'd have to use force.

"Well I suppose I have fibbed once or twice. But you know what Naruto, he's been liein to you your whole life."

"Mizuki don't you dare!" Iruka shouted and lunged forward, his kunai drawn.

Mizuki leapt out of the way and brought out his own kunai, to block the coming slash.

"That's right Naruto, he's not even your real dad,"

It felt like he had been punched in the gut, "what?" he looked to his … father figure to see if it was true and all he saw was rage

"Naruto don't listen just run."

"Oh, but then he'd miss the best part!"

"If you say one more word Mizuki!" The Chunin didn't even flinch at the threat but instead slammed his body into Iruka, knocking them both to the ground.

"Naruto, what happened on the day you were born? I know you know."

Mizuki leapt over Iruka's strike, he was too angry to focus on him. The attacking Chunin took a breath and lunged for Mizuki again.

Naruto knew. Mizuki had drilled it into his head. That was the day His mother died, the day the Kyuubi attacked.

"The Yondaime couldn't kill it, so instead he used an orphan child to seal it! Iruka was assigned to keep you from hurting anyone."

"It's your fault his parents are un-avenged, and he hates you for it! that's why he never passed you. You killed every one he ever cared about!"

Naruto couldn't move, he felt like he would puke. He knew what that meant he understood the concept. All he could do was watch as his so called father finally caught Mizuki and tore him to pieces.

Naruto couldn't take it, he couldn't watch as his best friend and second role model died, so he created a dozen clones and fled in every direction.

0o0o0

That day, the day he lost every thing and found the one thing that meant everything to him now.

That day was the day he first met His son, the day he first read his favorite book; he had been half way through it when the three of them arrived at the birthing room. Lady Kushina the hokage's wife herself was the woman he had been following around all day, he didn't let on that he had found out. So when it began he sat out in the hall as he watched several others come and go.

Then as he turned the last page everything became chaos, he was hit by flying debris, as the wall behind him exploded and the beast appeared. It was a monster, which had ripped itself out of the flesh of Lady Kushina. The Yondaime teleported both her and the baby out of the room. And then, he felt himself yanked backwards and was all the way on the other side of the village. He watched in horror as the beast, the Kyuubi destroyed everything. Then it was simply gone. By the time he made it there the third had already taken hold of the baby, and anounded that the fourth was dead!

0o0o0

Iruka ran, he chased after Naruto, even with so many shodow clones he couldn't fool him. He knew where the real one would be.

"It not true is it … D-Dad? Is it?" Naruto was crying, his knees held to his chest by his arms, on his favorite spot in the whole village.

"Naruto, I promised to keep you safe. When your father used you to seal away the demon, I swore to your mother I would raise you to be the ninja she always wanted you to become."

His eyes grew wide at that "My father? Then it is true your not – not…" He let out a sob and buried his face in his arms.

"No, I'm not. But I wanted to be. I love you, and I loved your mother. If not for you, I wouldn't have been able to go on after what happened."

"But, I – I hold _**IT!**_ How could you not hate me?"

"Because you keep it at bay. You are the prison and every day you live it is paying for its crimes. You are the son of the Fourth Hokage, you are the prison that saved the village from the Kyuubi, you are my hero and one day you'll be my Hokage as well. And until that day even if not by blood you will always be my son."

Naruto looked up into the eyes of the first person to ever honestly say he would be Hokage. And he knew his father wasn't lying.

It took almost twenty minutes for Iruka to pry himself out of the hug his son had him in. And once he did he told him that he was going to be one hell of a genin for the next year or so.

* * *

-Note- The turning point was when the Fourth Hokage decided to put all active shinobi on guard and duty, and have the academy students perform the D-ranks for the day.

and also, before his parents died Iruka was a good student, it doesn't tell us how good or anything so I decided that on my own.

While Retro will be my main Fic, Four others are on my list to work on at the moment: Life After The Ends; Lone Fox; The Thousand Ninja; and Village Hidden in Plain Sight. Descriptions on profile.


End file.
